Yes, I had a problem with one of my websites that has an SSL certificate. We were ranking miserably low despite our efforts to optimize the site. It turned out that we were creating duplicate content with the certificate, that is, all our pages appeared in both http and https. We fixed it by putting 2 htaccess files, one inside and one outside the folder that contains the secure content. Perhaps it's not the best thing to do, but it worked. We finally got indexed by G. Look for a post that says something like "canonicalization issues" and you'll find several ways to fix the issue, among them the code I used which is good for GoDaddy hosting and their SSL.